In recent years, developments in the field of synthetic biology have allowed researchers to synthesize a number of intermediates with potential applications in, for instance, the bio-energy or pharmaceuticals fields, by changing bacterial or cellular metabolic processes. For example, in 2006, scientists used engineered yeast to synthesize artemisinin intermediates, increasing the yield to reach 115 mg/mL (Ro, D. K. et al. Nature, 2006, 440: 940-943). In 2009, George Church's group accelerated the evolution of E. coli to increase the yield of lycopene by fivefold, through introducing a set of oligonucleotides to modify the bacteria's genome (Wang, H. et al. Nature, 2009, 460: 894-898).
Scientists have also begun synthesizing complete genomes for living organisms. In 2008, the genome of Mycoplasma Genitalium, measuring 582 kb in length, was successfully synthesized. In 2010, scientists assembled a modified genome of about one million base pairs, and used it to produce a self-replicating Mycoplasma Mycoides (Gibson, D, et al. Science, 2010, 329:52-56.
One key development which has prompted significant growth in the field of synthetic biology is the maturation of gene synthesis technology. In recent years, DNA microarray technology has given researchers the ability to synthesize genes on a large scale. Indeed, at present, one microarray can synthesize millions of oligonucleotides. However, the lengths of these oligonucleotides range generally between 60 bp to 200 bp. Assembling these oligonucleotides into genes with sufficient length (i.e., greater than 1 kb) is a current challenge to researchers, particularly in circumstances where thousands of long-chain genes are needed.
Currently, there exist two related strategies for addressing these problems. The first is to continue to improve synthesis techniques and develop new approaches to increasing the length of each oligonucleotide. The second is to develop an effective method to assemble millions of short oligonucleotides into long-chain genes in parallel. However, the first strategy depends on, and is still awaiting, further breakthroughs in new technologies. And while there has been some development with regards to the second strategy, these established approaches still have certain drawbacks. For instance, Church successfully synthesized 47 genes (measuring 35 kb) by selectively amplifying and assembling a group of microchip-synthesized oligonucleotides (Kosuri, S. et al. Nature Biotechnology, 2010, 28(12):1295-1299). Church accomplished this by assembling a group of amplified oligonucleotides into a long-chain nucleotide sequence using a DNA microchip. Jingdong Tian's group also achieved synthesis of 74 genes (measuring 30 kb) by dividing a microarray into distinct physical units, and then performing parallel synthesis, amplification and assembly (Quan, J. et al. Nature Biotechnology, 2011, 29(5):448-452. However, both methods are not only very costly, but are also limited in synthetic throughput.
This present application describes simpler and more feasible systems and methods for synthetically assembling thousands of oligonucleotides into multiple nucleotide sequences in parallel.